Compositions and methods for characterizing and restoring gastrointestinal, skin, and nasal microbiota

Abstract

The present invention relates to characterizing changes in mammalian bacterial gastrointestinal, cutaneous and nasal microbiota associated with antibiotic treatment and various disease conditions (such as asthma, allergy, obesity, metabolic syndrome, gastrointestinal reflux disease (GERD), eosinophilic esophagitis, gastro-esophageal junction adenocarcinomas (GEJAC), infections due to bacteria that are resistant to antibiotics, including Methicillin-resistant Staphylococcus aureus (MRSA), Clostridium difficile, vancomycin-resistant enterococci, etc.) and related diagnostic and therapeutic methods. Therapeutic methods of the invention involve the use of live bacterial inoculants that are capable of restoring healthy mammalian bacterial gastrointestinal, skin, and nasal microbiota.

Description

CROSS REFERENCE TO RELATED APPLICATIONS[0001]The present application claims priority to U.S. Provisional Patent Application Ser. No. 61 / 100,172, filed Sep. 25, 2008, and U.S. Provisional Patent Application Ser. No. 61 / 181,970, filed May 28, 2009, both of which are hereby incorporated by reference in their entireties.FIELD OF THE INVENTION[0002]The present invention relates to characterizing changes in mammalian bacterial gastrointestinal, cutaneous (skin) and nasal microbiota associated with antibiotic treatment and various disease conditions (such as asthma, allergy, obesity, metabolic syndrome, insulin-deficiency or insulin-resistance related disorders, ischemia, oxidative stress, atherosclerosis, hypertension, abnormal lipid metabolism, gastrointestinal reflux disease (GERD), eosinophilic esophagitis, gastro-esophageal junction adenocarcinomas (GEJAC), infections due to bacteria that are resistant to antibiotics, including Methicillin-resistant Staphylococcus aureus (MRSA), Clost...

AI Technical Summary

Benefits of technology

[0034]In another specific embodiment, the invention provides that the total number of Butyryl CoA transferase (BCoAT)-encoding genes (i.e., genes encoding an enzyme involved in the regulation of metabolism of short chain fatty acids and specifically butyrate synthesis) is increased in mammalian bacterial gastrointestinal microbiota upon treatment with sub-therapeutic doses of antibiotics, wherein such treatment is associated with increased % body fat and adipose tissue deposition. Thus, the present invention provides a diagnostic of obesity based on screening for increased number of Butyryl CoA transferase (BCoAT)-encoding genes (or other genes encoding an enzyme involved in the regulation of metabolism of short chain fatty acids (SCFA) and, preferably, butyrate synthesis) in mammalian bacterial gastrointestinal microbiota.

[0041]In certain embodiments, the probiotic composition of the invention comprises a therapeutically effective amount of at least one bacterial strain, or combinations of several strains, wherein the composition inhibits the growth of antibiotic-resistant bacteria. In a specific embodiment, such composition comprises one or several antibiotic-sensitive bacterial strains which have been diminished or lost as a result of antibiotic treatment. In one embodiment, such antibiotic-sensitive bacteria are capable of competing with antibiotic-resistant bacteria that facilitate calorie uptake in the gut and in this way lower weight gain by the host and treat obesity, metabolic syndrome, diabetes, and related disorders. In another embodiment, such antibiotic-sensitive bacteria are capable of competing with antibiotic-resistant bacteria and facilitate T regulatory responses in gastric and / or intestinal tissue and in this way treat asthma, allergy and related disorders (e.g., eczema, allergic rhinitis, etc.).

Problems solved by technology

However, neither of these alone or together are sufficient to explain the rise in obesity and subsequent or concomitant obesity-related disorders, such as, e.g., type II diabetes mellitus, metabolic syndrome, hypertension, cardiac pathology, and non-alcoholic fatty liver disease.

However, none of these can fully explain the rise in GERD and its related conditions across widespread population groups.

An alternative explanation is that the GERD is due to the growing epidemic of obesity, but since many non-obese persons suffer from GERD, this also is insufficient to explain the explosive rise in GERD and related esophageal diseases.

Similarly, childhood-onset asthma and related disorders including allergic rhinitis (“hay fever”) and eczema (atopic dermatitis) are also becoming increasingly important medical problems in the United States and other developed countries.

However, none of these are sufficient to explain the rise in asthma and its related conditions across widespread population groups.

An alternative explanation is that the lack of exposures to environmental microbes, such as those found in soil, in pets, and in farm animals is responsible for the rise in asthma (often called the “hygiene hypothesis”), but this too is insufficient to explain the explosive rise in asthma, especially that which begins in early childhood.

Although certain bacterial associations have been examined for these conditions, the role of bacterial microbiota in ailments such as asthma, obesity, GERD and certain related cancers, all of which have been on the rise in the 21st century, has not been clearly understood or appreciated.

While the microbiota is highly extensive, it is barely characterized.

However, many of the natural mechanisms for the transmission of these indigenous organisms across generations and between family members have diminished with socioeconomic development.

Images